The present invention relates generally to methods of measuring nucleic acid molecules in a target and more specifically to methods of detecting differential gene expression.
Every living organism requires genetic material, deoxyribonucleic acid (DNA), which contains genes that impart a unique collection of characteristics to the organism. DNA is composed of two strands of complementary sequences of nucleotide building blocks. The two strands bind, or hybridize, with the complementary sequence to form a double helix. Genes are discreet segments of the DNA and provide the information required to generate a new organism and to give that organism its unique characteristics. Even simple organisms, such as bacteria, contain thousands of genes, and the number is many fold greater in complex organisms such as humans. Understanding the complexities of the development and functioning of living organisms requires knowledge of these genes.
For many years, scientists have searched for and identified a number of genes important in the development and function of living organisms. The search for new genes has greatly accelerated in recent years due to directed projects aimed at identifying genetic information with the ultimate goal being the determination of the entire genome of an organism and its encoded genes, termed genomic studies. One of the most ambitious of these genomic projects has been the Human Genome Project, with the goal of sequencing the entire human genome. Recent advances in sequencing technology have led to a rapid accumulation of genetic information, which is available in both public and private databases. These newly discovered genes as well as those genes soon to be discovered provide a rich resource of potential targets for the development of new drugs.
Despite the rapid pace of gene discovery, there remains a formidable task of characterizing these genes and determining the biological function of these genes. The characterization of newly discovered genes is often a time consuming and laborious undertaking, sometimes taking years to determine the function of a gene or its gene product, particularly in complex higher organisms.
Another level of complexity arises when complex interactions between genes and their gene products are contemplated. To understand how an organism works, it is important not only to understand what role a gene, its transcript and its gene product plays in the workings of an organism, it is also important to understand potentially complex interactions between the gene, its transcript, or its gene product and other genes and their gene products.
A number of approaches have been used to assess gene expression in a particular cell or tissue of an organism. These approaches have been used to characterize gene expression under various conditions, including looking at differences in expression under differing conditions. However, most of these methods are useful for detecting transcripts that are abundant transcripts but have proven less useful for detecting transcripts that are of low abundance, particularly when looking at the expression of a number of genes rather than a selected few genes. Since genes expressed at low levels often regulate the physiological pathways in a cell, it is desirable to detect transcripts having at low abundance.
Thus, a need exists for a method to characterize the expression pattern of genes under a given set of conditions and to detect low abundance transcripts. The present invention satisfies this need and provides related advantages as well.
The invention provides a method of measuring the level of two or more nucleic acid molecules in a target by contacting a probe with a target comprising two or more nucleic acid molecules, wherein the nucleic acid molecules are arbitrarily sampled and wherein the arbitrarily sampled nucleic acid molecules comprise a subset of the nucleic acid molecules in a population of nucleic acid molecules; and detecting the amount of specific binding of the target to the probe. The invention also provides a method of measuring the level of two or more nucleic acid molecules in a target by contacting a probe with a target comprising two or more nucleic acid molecules, wherein the nucleic acid molecules are statistically sampled and wherein the statistically sampled nucleic acid molecules comprise a subset of the nucleic acid molecules in a population of nucleic acid molecules; and detecting the amount of specific binding of the target to the probe.